libpappsomspp
Library for mass spectrometry
pappso::Utils Class Reference

#include <utils.h>

Static Public Member Functions

static const QString getLexicalOrderedString (unsigned int num)
 
static void writeLexicalOrderedString (QTextStream *p_out, unsigned int num)
 
static int zeroDecimalsInValue (pappso_double value)
 0.11 would return 0 (no empty decimal) 2.001 would return 2 1000.0001254 would return 3 More...
 
static pappso_double roundToDecimals (pappso_double value, int decimal_places)
 
static long long int roundToDecimal32bitsAsLongLongInt (pappso::pappso_double input)
 
static std::string toUtf8StandardString (const QString &text)
 
static bool writeToFile (const QString &text, const QString &file_name)
 
static bool appendToFile (const QString &text, const QString &file_name)
 
static std::size_t extractScanNumberFromMzmlNativeId (const QString &spectrum_native_id)
 
static QString pointerToString (const void *const pointer)
 
static bool almostEqual (double value1, double value2, int decimalPlaces=10)
 
static double nearestGreater (double value)
 
static QString chronoTimePointDebugString (const QString &msg, std::chrono::system_clock::time_point chrono_time=std::chrono::system_clock::now())
 
static QString chronoIntervalDebugString (const QString &msg, std::chrono::system_clock::time_point chrono_start, std::chrono::system_clock::time_point chrono_finish=std::chrono::system_clock::now())
 
static std::vector< double > splitMzStringToDoubleVectorWithSpaces (const QString &text, std::size_t &error_count)
 
static std::vector< std::size_t > splitSizetStringToSizetVectorWithSpaces (const QString &text, std::size_t &error_count)
 
static QString booleanToString (bool value)
 convenient function to transform a boolean to QString "TRUE" or "FALSE" QString returned is readable by R More...
 

Static Public Attributes

static QRegularExpression xyMassDataFormatRegExp
 
static QRegularExpression mzListDataFormatRegExp
 Regular expression matching <m/z value><non-numerical*> More...
 
static QRegularExpression sizetListDataFormatRegExp
 Regular expression matching <size_t><non-numerical*> More...
 
static QRegularExpression endOfLineRegExp = QRegularExpression("^\\s+$")
 Regular expression that tracks the end of line in text files. More...
 

Detailed Description

Definition at line 48 of file utils.h.

Member Function Documentation

◆ almostEqual()

bool pappso::Utils::almostEqual ( double  value1,
double  value2,
int  decimalPlaces = 10 
)
static

Tell if both double values, are equal within the double representation capabilities of the platform.

Definition at line 260 of file utils.cpp.

261 {
262  // QString value1String = QString("%1").arg(value1,
263  // 0, 'f', 60);
264  // QString value2String = QString("%1").arg(value2,
265  // 0, 'f', 60);
266 
267  // qWarning() << __FILE__ << __LINE__ << __FUNCTION__
268  //<< "value1:" << value1String << "value2:" << value2String;
269 
270  // The machine epsilon has to be scaled to the magnitude of the values used
271  // and multiplied by the desired precision in ULPs (units in the last place)
272  // (decimal places).
273 
274  double valueSum = std::abs(value1 + value2);
275  // QString valueSumString = QString("%1").arg(valueSum,
276  // 0, 'f', 60);
277 
278  double valueDiff = std::abs(value1 - value2);
279  // QString valueDiffString = QString("%1").arg(valueDiff,
280  // 0, 'f', 60);
281 
282  double epsilon = std::numeric_limits<double>::epsilon();
283  // QString epsilonString = QString("%1").arg(epsilon,
284  // 0, 'f', 60);
285 
286  double scaleFactor = epsilon * valueSum * decimalPlaces;
287  // QString scaleFactorString = QString("%1").arg(scaleFactor,
288  // 0, 'f', 60);
289 
290  // qWarning() << "valueDiff:" << valueDiffString << "valueSum:" <<
291  // valueSumString <<
292  //"epsilon:" << epsilonString << "scaleFactor:" << scaleFactorString;
293 
294  bool res = valueDiff < scaleFactor
295  // unless the result is subnormal:
296  || valueDiff < std::numeric_limits<double>::min();
297 
298  // qWarning() << __FILE__ << __LINE__ << __FUNCTION__
299  //<< "returning res:" << res;
300 
301  return res;
302 }

References pappso::res.

◆ appendToFile()

bool pappso::Utils::appendToFile ( const QString &  text,
const QString &  file_name 
)
static

Definition at line 194 of file utils.cpp.

195 {
196 
197  QFile file(file_name);
198 
199  if(file.open(QFile::WriteOnly | QFile::Append))
200  {
201 
202  QTextStream out(&file);
203 
204  out << text;
205 
206  out.flush();
207  file.close();
208 
209  return true;
210  }
211 
212  return false;
213 }

◆ booleanToString()

QString pappso::Utils::booleanToString ( bool  value)
static

convenient function to transform a boolean to QString "TRUE" or "FALSE" QString returned is readable by R

Returns
QString "TRUE" or "FALSE"

Definition at line 423 of file utils.cpp.

424 {
425  if(value)
426  return "TRUE";
427  return "FALSE";
428 }

◆ chronoIntervalDebugString()

QString pappso::Utils::chronoIntervalDebugString ( const QString &  msg,
std::chrono::system_clock::time_point  chrono_start,
std::chrono::system_clock::time_point  chrono_finish = std::chrono::system_clock::now() 
)
static

Definition at line 329 of file utils.cpp.

333 {
334  QString debug_text =
335  QString(
336  "%1 %2 min = %3 s = %4 ms = %5 "
337  "µs\n")
338  .arg(msg)
339  .arg(std::chrono::duration_cast<std::chrono::minutes>(chrono_finish -
340  chrono_start)
341  .count())
342  .arg(std::chrono::duration_cast<std::chrono::seconds>(chrono_finish -
343  chrono_start)
344  .count())
345  .arg(std::chrono::duration_cast<std::chrono::milliseconds>(chrono_finish -
346  chrono_start)
347  .count())
348  .arg(std::chrono::duration_cast<std::chrono::microseconds>(chrono_finish -
349  chrono_start)
350  .count());
351 
352  return debug_text;
353 }

◆ chronoTimePointDebugString()

QString pappso::Utils::chronoTimePointDebugString ( const QString &  msg,
std::chrono::system_clock::time_point  chrono_time = std::chrono::system_clock::now() 
)
static

Definition at line 313 of file utils.cpp.

315 {
316 
317  time_t tt;
318 
319  tt = std::chrono::system_clock::to_time_t(chrono_time);
320 
321  QString debug_text =
322  QString("%1 - %2\n").arg(msg).arg(QString::fromLatin1(ctime(&tt)));
323 
324  return debug_text;
325 }

◆ extractScanNumberFromMzmlNativeId()

std::size_t pappso::Utils::extractScanNumberFromMzmlNativeId ( const QString &  spectrum_native_id)
static

TODO activate this in a future release to ensure scan number for(auto i = 0; i < native_id_list.size(); i += 2) { if(native_id_list[i] == "scan") { return native_id_list[i + 1].toULong(); } }

throw ExceptionNotFound( QObject::tr("scan number not found in mzML native id %1") .arg(spectrum_native_id));

Definition at line 217 of file utils.cpp.

218 {
219  qDebug() << " " << spectrum_native_id;
220  QStringList native_id_list = spectrum_native_id.split("=");
221  if(native_id_list.size() < 2)
222  {
223  throw ExceptionNotFound(
224  QObject::tr("scan number not found in mzML native id %1")
225  .arg(spectrum_native_id));
226  }
227  else
228  {
229  /** TODO activate this in a future release to ensure scan number
230  for(auto i = 0; i < native_id_list.size(); i += 2)
231  {
232  if(native_id_list[i] == "scan")
233  {
234  return native_id_list[i + 1].toULong();
235  }
236  }
237 
238  throw ExceptionNotFound(
239  QObject::tr("scan number not found in mzML native id %1")
240  .arg(spectrum_native_id));
241 
242 */
243  return native_id_list.back().toULong();
244  }
245  return 0;
246 }

◆ getLexicalOrderedString()

const QString pappso::Utils::getLexicalOrderedString ( unsigned int  num)
static

Definition at line 52 of file utils.cpp.

53 {
54  int size = log10(num);
55  size += 97;
56  QString base(size);
57  base.append(QString().setNum(num));
58  return (base);
59 }

References pappso::log10.

Referenced by pappso::GrpGroup::getGroupingId(), pappso::GrpPeptide::getGroupingId(), pappso::GrpProtein::getGroupingId(), pappso::GrpSubGroup::getGroupingId(), pappso::PwizMsFileReader::getMsRunIds(), and pappso::XyMsFileReader::getMsRunIds().

◆ nearestGreater()

double pappso::Utils::nearestGreater ( double  value)
static

Definition at line 306 of file utils.cpp.

307 {
308  return std::nextafter(value, value + 1);
309 }

◆ pointerToString()

QString pappso::Utils::pointerToString ( const void *const  pointer)
static

Definition at line 250 of file utils.cpp.

251 {
252  return QString("%1").arg(
253  (quintptr)pointer, QT_POINTER_SIZE * 2, 16, QChar('0'));
254 }

Referenced by pappso::QualifiedMassSpectrum::toString(), and pappso::MsRunDataSetTreeNode::toString().

◆ roundToDecimal32bitsAsLongLongInt()

long long int pappso::Utils::roundToDecimal32bitsAsLongLongInt ( pappso::pappso_double  input)
static

Definition at line 130 of file utils.cpp.

131 {
132  pappso::pappso_double test_decimal = 100000000000;
133  if(sizeof(int *) == 4)
134  { // 32bits
135  test_decimal = 100000000;
136  }
137  return (floor(input * test_decimal));
138 }
double pappso_double
A type definition for doubles.
Definition: types.h:48

◆ roundToDecimals()

pappso_double pappso::Utils::roundToDecimals ( pappso_double  value,
int  decimal_places 
)
static

Definition at line 119 of file utils.cpp.

120 {
121  if(decimal_places < 0)
122  return value;
123 
124  return ceil((value * pow(10, decimal_places)) - 0.49) /
125  pow(10, decimal_places);
126 }

Referenced by pappso::MassSpectrumMinusCombiner::combine(), pappso::MassSpectrumPlusCombiner::combine(), pappso::TraceMinusCombiner::combine(), and pappso::TracePlusCombiner::combine().

◆ splitMzStringToDoubleVectorWithSpaces()

std::vector< double > pappso::Utils::splitMzStringToDoubleVectorWithSpaces ( const QString &  text,
std::size_t &  error_count 
)
static

Definition at line 357 of file utils.cpp.

359 {
360 
361  QStringList string_list =
362  text.split(QRegularExpression("[\\s]+"), Qt::SkipEmptyParts);
363 
364  // qDebug() << "string list:" << string_list;
365 
366  std::vector<double> double_vector;
367 
368  for(int iter = 0; iter < string_list.size(); ++iter)
369  {
370  QString current_string = string_list.at(iter);
371 
372  bool ok = false;
373 
374  double current_double = current_string.toDouble(&ok);
375 
376  if(!current_double && !ok)
377  {
378  ++error_count;
379  continue;
380  }
381 
382  double_vector.push_back(current_double);
383  }
384 
385  return double_vector;
386 }

◆ splitSizetStringToSizetVectorWithSpaces()

std::vector< std::size_t > pappso::Utils::splitSizetStringToSizetVectorWithSpaces ( const QString &  text,
std::size_t &  error_count 
)
static

Definition at line 390 of file utils.cpp.

392 {
393  // qDebug() << "Parsing text:" << text;
394 
395  QStringList string_list =
396  text.split(QRegularExpression("[\\s]+"), Qt::SkipEmptyParts);
397 
398  // qDebug() << "string list size:" << string_list.size()
399  //<< "values:" << string_list;
400 
401  std::vector<std::size_t> sizet_vector;
402 
403  for(int iter = 0; iter < string_list.size(); ++iter)
404  {
405  QString current_string = string_list.at(iter);
406 
407  bool ok = false;
408 
409  std::size_t current_sizet = current_string.toUInt(&ok);
410 
411  if(!current_sizet && !ok)
412  {
413  ++error_count;
414  continue;
415  }
416 
417  sizet_vector.push_back(current_sizet);
418  }
419 
420  return sizet_vector;
421 }

◆ toUtf8StandardString()

std::string pappso::Utils::toUtf8StandardString ( const QString &  text)
static

Definition at line 142 of file utils.cpp.

143 {
144  std::string env_backup = setlocale(LC_ALL, "");
145 
146  // struct lconv *lc_backup = localeconv();
147  // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()"
148  //<< "env_backup=" << env_backup.c_str() << "lc_backup->decimal_point"
149  //<< lc_backup->decimal_point;
150 
151  // Force locale to be "C".
152  setlocale(LC_ALL, "C");
153 
154  // Now perform the conversion.
155  QByteArray byte_array = text.toUtf8();
156  std::string stdText = "";
157 
158  for(char c : byte_array)
159  {
160  stdText += c;
161  }
162 
163  // Set back the locale to the backed-up one.
164  setlocale(LC_ALL, env_backup.c_str());
165 
166  return stdText;
167 }

References pappso::c.

Referenced by pappso::PwizMsFileReader::initialize(), and pappso::PwizMsRunReader::initialize().

◆ writeLexicalOrderedString()

void pappso::Utils::writeLexicalOrderedString ( QTextStream *  p_out,
unsigned int  num 
)
static

Definition at line 63 of file utils.cpp.

64 {
65  *p_out << (char)(log10(num) + 97) << num;
66 }

References pappso::log10.

◆ writeToFile()

bool pappso::Utils::writeToFile ( const QString &  text,
const QString &  file_name 
)
static

Definition at line 171 of file utils.cpp.

172 {
173 
174  QFile file(file_name);
175 
176  if(file.open(QFile::WriteOnly | QFile::Truncate))
177  {
178 
179  QTextStream out(&file);
180 
181  out << text;
182 
183  out.flush();
184  file.close();
185 
186  return true;
187  }
188 
189  return false;
190 }

◆ zeroDecimalsInValue()

int pappso::Utils::zeroDecimalsInValue ( pappso_double  value)
static

0.11 would return 0 (no empty decimal) 2.001 would return 2 1000.0001254 would return 3

Determine the number of zero decimals between the decimal point and the first non-zero decimal.

Parameters
valuethe value to be analyzed
Returns
the number of '0' decimals between the decimal separator '.' and the first non-0 decimal

Definition at line 81 of file utils.cpp.

82 {
83  //qDebug() << qSetRealNumberPrecision(10) << "Double value: " << value;
84 
85  int intPart = static_cast<int>(value);
86 
87  //qDebug() << "int part:" << intPart;
88 
89  double decimalPart = value - intPart;
90 
91  //qDebug() << qSetRealNumberPrecision(10) << "decimal part: " << decimalPart;
92 
93  int count = 0;
94 
95  while(decimalPart > 0)
96  {
97  ++count;
98 
99  decimalPart *= 10;
100 
101  //qDebug() << "Iteration " << count << "decimal part:" << decimalPart;
102 
103  if(decimalPart >= 1)
104  {
105  //qDebug() << "Because decimal part " << decimalPart
106  //<< "is >= 1, breaking loop while count is " << count << ".";
107 
108  break;
109  }
110  }
111 
112  //qDebug() << "Returning count:" << count;
113 
114  return count;
115 }

Referenced by pappso::MzIntegrationParams::createArbitraryBins().

Member Data Documentation

◆ endOfLineRegExp

QRegularExpression pappso::Utils::endOfLineRegExp = QRegularExpression("^\\s+$")
static

Regular expression that tracks the end of line in text files.

Definition at line 62 of file utils.h.

Referenced by pappso::XyMsRunReader::accept(), pappso::XyMsFileReader::initialize(), and pappso::XyMsRunReader::qualifiedMassSpectrumFromXyMSDataFile().

◆ mzListDataFormatRegExp

QRegularExpression pappso::Utils::mzListDataFormatRegExp
static

Regular expression matching <m/z value><non-numerical*>

Definition at line 56 of file utils.h.

◆ sizetListDataFormatRegExp

QRegularExpression pappso::Utils::sizetListDataFormatRegExp
static

Regular expression matching <size_t><non-numerical*>

Definition at line 59 of file utils.h.

◆ xyMassDataFormatRegExp

QRegularExpression pappso::Utils::xyMassDataFormatRegExp
static
Initial value:
=
QRegularExpression("^(\\d*\\.?\\d+)([^\\d^\\.^-]+)(-?\\d*\\.?\\d*[e-]?\\d*)")

Regular expression matching <numerical value><non-numerical*><numerical value>

Definition at line 53 of file utils.h.

Referenced by pappso::XyMsRunReader::accept(), pappso::XyMsFileReader::initialize(), pappso::DataPoint::initialize(), and pappso::XyMsRunReader::qualifiedMassSpectrumFromXyMSDataFile().


The documentation for this class was generated from the following files: